Molecular Karyotyping: Array CGH Quality Criteria for Constitutional Genetic Diagnosis

Abstract

S U M M A R YArray CGH (comparative genomic hybridization) enables the identification of chromosomal copy number changes. The availability of clone sets covering the human genome opens the possibility for the widespread use of array CGH for both research and diagnostic purposes. In this manuscript we report on the parameters that were critical for successful implementation of the technology, assess quality criteria, and discuss the potential benefits and pitfalls of the technology for improved pre-and postnatal constitutional genetic diagnosis. We propose to name the genome-wide array CGH "molecular karyotyping," in analogy with conventional karyotyping that uses staining methods to visualize chromosomes.

Genome-wide arrays: Quality criteria and platforms to be used in routine diagnostics

“…These are discussed in more detail below. Quality criteria for genomic arrays have been published [Fiegler et al, 2006;Vermeesch et al, 2005Vermeesch et al, , 2007. These recommendations were based on the use of bacterial artificial chromosome arrays, but the general principles apply to oligonucleotide and SNP arrays too.…”

“…Higher SDs lower the operational resolution of an array and can result in an increased number of false-positive calls. With low SDs, a smaller number of targets deviating from normal can be called copy number variable with confidence (for the theoretical approach, see Vermeesch et al, 2005).…”

A syndrome of short stature, microcephaly and speech delay is associated with duplications reciprocal to the common Sotos syndrome deletion

“…23 DNA from Case 2 was hybridized to a custom BAC-emulated oligonucleotide array (Agilent Technologies, Santa Clara, CA, USA). The array comprises a total of 42 640 oligonucleotide probes localized to the genomic positions of 1400 FISH-verified bacterial artificial chromosome (BAC) clones covering more than 140 regions implicated in genetic diseases, as well as clinically relevant subtelomeric and pericentromeric regions.…”

Array-based comparative genomic hybridization of mapped BAC DNA clones to screen for chromosome 14 copy number abnormalities in meningiomas

“…Adjacent and overlapping clones can be used together to increase the efficiency and accuracy of the analysis, as the tile-path array in which a set of overlapping clones are used, deletions or gains larger than or equal to a single clone, frequently involve also neighbouring clones. 21 In this study, we used a total of 807 BAC clones to map the long arm of chromosome 14; with such clones, insert sizes of between 100 and 300 kb were obtained which would allow the identification of altera- tions in relatively small regions. To avoid overinterpretation of changes at single clones due to the technical artefacts, 18 CNV were only defined when altered fluorescence ratios were observed in two or more consecutive clones.…”